The guanine nucleotide dissociation inhibitor (GDI) regulates the retrieval of Rab GTPases in vesicular traffic, while inhibiting GDP dissociation from Rabs. The soluble complex, GDI-Rab, serves as a cytosolic reservoir for the delivery of Rab to newly formed vesicles, where the Rab protein is activated to the GTP form. The crystal structure of this 55 kDa protein had been previously determined to 1.8 E resolution. The SSRL beamline 9-1 was optimized at a wavelength 0.79 E, which allowed us to collect an ultra high resolution data set to 1.04 E at -176 C. High and medium (1.4 E) resolution data sets were collected from a single crystal and the data were merged and processed using MOLSFLM with an overall Rmerge of 7% (all data). Refinement was carried out using SHELXL-97 which, at this resolution, allowed us to perform individual anisotropic thermal displacement parameter refinement. A number of residues were found to possess multiple conformations and some incorrect rotomers were identified, particularly for leucine residues. In addition, the His-tagged residues at the N terminus that were used for purification purpose could now be clearly identified in the electron density map. Over 400 water molecules were added stepwise during the refinement and hydrogens were positioned towards the end of refinement. The current Rcryst and Rfree values are 15.6% and 19.0%, respectively.